Whole-genome sequencing (WGS) information has played a crucial role in the SARS-CoV-2 (COVID-19) pandemic by providing evidence about variants to inform public health policy. The purpose of this ...study was to assess the representativeness of sequenced cases compared with all COVID-19 cases in England, between March 2020 and August 2021, by demographic and socio-economic characteristics, to evaluate the representativeness and utility of these data in epidemiological analyses. To achieve this, polymerase chain reaction (PCR)-confirmed COVID-19 cases were extracted from the national laboratory system and linked with WGS data. During the study period, over 10% of COVID-19 cases in England had WGS data available for epidemiological analysis. With sequencing capacity increasing throughout the period, sequencing representativeness compared to all reported COVID-19 cases increased over time, allowing for valuable epidemiological analyses using demographic and socio-economic characteristics, particularly during periods with emerging novel SARS-CoV-2 variants. This study demonstrates the comprehensiveness of England’s sequencing throughout the COVID-19 pandemic, rapidly detecting variants of concern, and enabling representative epidemiological analyses to inform policy.
Toxoplasma gondii is a protozoan pathogen that widely affects the human population. The current antibiotics used for treating clinical toxoplasmosis are limited. In addition, they exhibit adverse ...side effects in certain groups of people. Therefore, discovery of novel therapeutics for clinical toxoplasmosis is imperative. The first step of novel antibiotic development is to identify chemical compounds showing high efficacy in inhibition of parasite growth using a high throughput screening strategy. As an obligate intracellular pathogen, Toxoplasma can only replicate within host cells, which prohibits the use of optical absorbance measurements as a quick indicator of growth. Presented here is a detailed protocol for a luciferase-based growth assay. As an example, this method is used to calculate the doubling time of wild-type Toxoplasma parasites and measure the efficacy of morpholinurea-leucyl-homophenyl-vinyl sulfone phenyl (LHVS, a cysteine protease-targeting compound) regarding inhibition of parasite intracellular growth. Also described, is a CRISPR-Cas9-based gene deletion protocol in Toxoplasma using 50 bp homologous regions for homology-dependent recombination (HDR). By quantifying the inhibition efficacies of LHVS in wild-type and TgCPL (Toxoplasma cathepsin L-like protease)-deficient parasites, it is shown that LHVS inhibits wild-type parasite growth more efficiently than Δcpl growth, suggesting that TgCPL is a target that LHVS binds to in Toxoplasma. The high sensitivity and easy operation of this luciferase-based growth assay make it suitable for monitoring Toxoplasma proliferation and evaluating drug efficacy in a high throughput manner.
PRIMARY CARE RESEARCH underpins the development and implementation of best clinical practice and health service delivery in the general practice setting. In Australia, general practice is the ...cornerstone of primary healthcare and primary medical care delivery. It is essential to involve primary healthcare professionals as stakeholders in the development of research questions and study design to ensure relevance and feasibility. Primary healthcare provider participation is key to providing research that can be readily translated to improve patient care. This commentary describes GP Circle, a unique initiative to integrate primary care professionals early in the development of cancer research.
Background. Tenofovir disoproxil fumarate (TDF) has been linked to renal impairment, but the extent to which this impairment is reversible is unclear. We aimed to investigate the reversibility of ...renal decline during TDF therapy. Methods. Cox proportional hazards models assessed factors associated with discontinuing TDF in those with an exposure duration of >6 months. In those who discontinued TDF therapy, linear piecewise regression models estimated glomerular filtration rate (eGFR) slopes before initiation of, during, and after discontinuation of TDF therapy. Factors associated with not achieving eGFR recovery 6 months after discontinuing TDF were assessed using multivariable logistic regression. Results. We observed declines in the eGFR during TDF exposure (mean slopes, -15.7 mL/minute/1.73 m²/year 95% confidence interval {CI}, -20.5 to -10.9 during the first 3 months and -3.1 mL/minute/1.73 m²/year 95% CI, -4.6 to -1.7 thereafter) and evidence of eGFR increases following discontinuation of TDF therapy (mean slopes, 12.5 mL/minute/1.73 m²/year 95% CI, 8.9-16.1 during the first 3 months and 0.8 mL/minute/1.73 m²/year 95% CI, .1-1.5 thereafter). Following TDF discontinuation, 38.6% of patients with a decline in the eGFR did not experience recovery. A higher eGFR at baseline, a lower eGFR after discontinuation of TDF therapy, and more-prolonged exposure to TDF were associated with an increased risk of incomplete recovery 6 months after discontinuation of TDF therapy. Conclusions. This study shows that a decline in the eGFR during TDF therapy was not fully reversible in one third of patients and suggests that prolonged TDF exposure at a low eGFR should be avoided.
Antimicrobial resistance is a serious threat to public health, with most antibiotics prescribed in primary care. General practitioners (GPs) report defensive antibiotic prescribing to mitigate ...perceived risk of future hospital admission in children with respiratory tract infections. We developed a clinical rule aimed to reduce clinical uncertainty by stratifying risk of future hospital admission.
8394 children aged between 3 months and 16 years presenting with acute cough (for ≤28 days) and respiratory tract infection were recruited to a prognostic cohort study from 247 general practitioner practices in England. Exposure variables included demographic characteristics, parent-reported symptoms, and physical examination signs. The outcome was hospital admission for respiratory tract infection within 30 days, collected using a structured, blinded review of medical records.
8394 (100%) children were included in the analysis, with 78 (0·9%, 95% CI 0·7%–1·2%) admitted to hospital: 15 (19%) were admitted on the day of recruitment (day 1), 33 (42%) on days 2–7; and 30 (39%) on days 8–30. Seven characteristics were independently associated (p<0·01) with hospital admission: age <2 years, current asthma, illness duration of 3 days or less, parent-reported moderate or severe vomiting in the previous 24 h, parent-reported severe fever in the previous 24 h or a body temperature of 37·8°C or more at presentation, clinician-reported intercostal or subcostal recession, and clinician-reported wheeze on auscultation. The area under the receiver operating characteristic (AUROC) curve for the coefficient-based clinical rule was 0·82 (95% CI 0·77–0·87, bootstrap validated 0·81). Assigning one point per characteristic, a points-based clinical rule consisting of short illness, temperature, age, recession, wheeze, asthma, and vomiting (mnemonic STARWAVe; AUROC 0·81, 0·76–0·85) distinguished three hospital admission risk strata: very low (0·3%, 0·2–0·4%) with 1 point or less, normal (1·5%, 1·0–1·9%) with 2 or 3 points, and high (11·8%, 7·3–16·2%) with 4 points or more.
Clinical characteristics can distinguish children at very low, normal, and high risk of future hospital admission for respiratory tract infection and could be used to reduce antibiotic prescriptions in primary care for children at very low risk.
National Institute for Health Research (NIHR).
In situ soft X-ray absorption spectroscopy (XAS) was employed to study the adsorption and dissociation of carbon monoxide molecules on cobalt nanoparticles with sizes ranging from 4 to 15 nm. The ...majority of CO molecules adsorb molecularly on the surface of the nanoparticles, but some undergo dissociative adsorption, leading to oxide species on the surface of the nanoparticles. We found that the tendency of CO to undergo dissociation depends critically on the size of the Co nanoparticles. Indeed, CO molecules dissociate much more efficiently on the larger nanoparticles (15 nm) than on the smaller particles (4 nm). We further observed a strong increase in the dissociation rate of adsorbed CO upon exposure to hydrogen, clearly demonstrating that the CO dissociation on cobalt nanoparticles is assisted by hydrogen. Our results suggest that the ability of cobalt nanoparticles to dissociate hydrogen is the main parameter determining the reactivity of cobalt nanoparticles in Fischer–Tropsch synthesis.
Climate change will likely impact rainfall characteristics in particular locations; the amount, seasonality, variability and spatial patterns. In developing countries, this presents challenges for ...rural smallholder farmers as their livelihoods are largely based on rain-fed practices. Changes in climate patterns could increase farmers' vulnerability and the need for intervention. In this paper, we develop new metrics of analysis motivated by qualitative research with smallholder farmers. Previous research found that farmers' understanding of historical rainfall change is accurate, yet diverge from some research studies. We analyze meteorological station rainfall data using metrics that are familiar to smallholders. Farmers' perceptions of rainfall in southern Ethiopia were explored through interviews conducted in three communities. Our findings identified some forms of convergence, as well as divergence, in farmers' perception of rainfall trends and meteorological station data results. In asking the question ‘Why do data based on farmer experiences of rainfall variability differ from meteorological station data?’, we show that using existing data and applying farmer-influenced metrics can improve the information shared with farmers. We argue that, under further climate change, it will be increasingly important to convey meteorological information to farmers in ways that are relevant to them and their agricultural livelihoods.
•Smallholder farmer experiences and climate science often diverge.•We develop new metrics motivated by research with smallholders.•New metrics and analyses can bridge some divergences.•Methods developed are relevant for communicating climate science with farmers.
Tire and road wear particles (TRWP) are formed at the frictional interface between tires and the road surface. Tire tread and road pavement materials are denser than water but can be washed from the ...road surface into receiving water bodies, ultimately depositing into sediment, soil, or other media depending on the receiving environment. However, the paucity of mass-based measurements has limited the knowledge on the nature and extent of environmental concentrations necessary for environmental risk assessment of TRWP. Surface water and sediment samples were collected from the Seine River, France to characterize TRWP concentration. Sample locations were established upstream, within, and downstream of a major metropolitan area (Paris); downstream of smaller urban areas; adjacent to undeveloped land; and near the confluence of the estuary. Surface water and sediment were collected from the left and right banks at each of the eight locations, including two duplicates, for a total of 18 samples. Additionally, three sediment traps were deployed near the mouth of the river to quantify the flux of TRWP to sediment. Retained solids and sediment samples were analyzed using a modified pyrolysis gas chromatography/mass spectrometry (Py-GC/MS) method that minimized the matrix interferences in the samples thus improving the current ISO Technical Specification ISO/TS 21396 : 2017 for TRWP mass concentration by Py-GC/MS. TRWP concentration was alternatively estimated by separating the sediment into the <1.9 g cm−3 fraction and analyzing for tread-derived zinc content. TRWP concentrations estimated by zinc method were significantly higher than results from the modified Py-GC/MS method. TRWP and total zinc concentrations show a decreasing trend from available historical data.
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•The first reported results of TRWP in retained solid samples collected from a river•TRWP concentrations in retained solids were significantly higher than in sediment.•(SBR/BR)/NR ratio was lower than expected based on passenger/truck tires literature.•First study to evaluate the temporal trend of TRWP in river sediment•Lower TRWP concentrations over time could indicate improvements in water quality.
Abstract
Background
Natural and vaccine-induced immunity will play a key role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. SARS-CoV-2 variants have the ...potential to evade natural and vaccine-induced immunity.
Methods
In a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, United Kingdom, we investigated the protection from symptomatic and asymptomatic polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after 1 versus 2 vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing.
Results
In total, 13 109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses), and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and 2 vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 95% confidence interval {CI} < .01–.18). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 95% CI .02–.38) and 85% (0.15 95% CI .08–.26), respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 95% CI .21–.52) and any PCR-positive result by 64% (0.36 95% CI .26–.50). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7.
Conclusions
Natural infection resulting in detectable anti-spike antibodies and 2 vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant.
Natural infection resulting in detectable anti-spike antibodies and two vaccine doses both provided ≥85% protection against symptomatic and asymptomatic SARS-CoV-2 infection in healthcare workers, including against the B.1.1.7 variant. Single dose vaccination reduced symptomatic infection by 67%.
Diagnostic uncertainty over respiratory tract infections (RTIs) in primary care contributes to over-prescribing of antibiotics and drives antibiotic resistance. If symptoms and signs predict ...respiratory tract microbiology, they could help clinicians target antibiotics to bacterial infection. This study aimed to determine relationships between symptoms and signs in children presenting to primary care and microbes from throat swabs.
Cross-sectional study of children ≥3 months to <16 years presenting with acute cough and RTI, with subset follow-up. Associations and area under receiver operating curve (AUROC) statistics sought between clinical presentation and baseline microbe detection. Microbe prevalence compared between baseline (symptomatic) and follow-up (asymptomatic) visits.
At baseline, ≥1 bacteria was detected in 1257/2113 (59.5%) children and ≥1 virus in 894/2127 (42%) children. Clinical presentation was not associated with detection of ≥1 bacteria AUROC 0.54 (95% CI 0.52-0.56) or ≥1 virus 0.64 (95% CI 0.61-0.66). Individually, only respiratory syncytial virus (RSV) was associated with clinical presentation AUROC 0.80 (0.77-0.84). Prevalence fell between baseline and follow-up; more so in viruses (68% versus 26%, P < 0.001) than bacteria (56% versus 40%, P = 0.01); greatest reductions seen in RSV, influenza B and Haemophilus influenzae.
Findings demonstrate that clinical presentation cannot distinguish the presence of bacteria or viruses in the upper respiratory tract. However, individual and overall microbe prevalence was greater when children were unwell than when well, providing some evidence that upper respiratory tract microbes may be the cause or consequence of the illness. If causal, selective microbial point-of-care testing could be beneficial.
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